Error while calculating TF-eGRNs AUC correlation

[Umaarasu]

Hi, Mid way through SCENIC analysis I got this error. Can someone help me with this. Thanks!

Traceback (most recent call last):
File "/SCENICplus_analysis/Scenic_script.py", line 58, in
raise(e)
File "/SCENICplus_analysis/Scenic_script.py", line 38, in
run_scenicplus(
File "/scenicplus/src/scenicplus/wrappers/run_scenicplus.py", line 244, in run_scenicplus
generate_pseudobulks(scplus_obj,
File "/scenicplus/src/scenicplus/cistromes.py", line 227, in generate_pseudobulks
sample_cells = sample(cells, nr_cells)
File "Groups/anaconda3/envs/scenicplus/lib/python3.8/random.py", line 363, in sample
raise ValueError("Sample larger than population or is negative")
ValueError: Sample larger than population or is negative

[SeppeDeWinter]

Hi @Umaarasu

See this comment: #87 (comment)

I will try to push another function this week that will solve this issue.
For now you can either skip this step or run the generate_pseudobulks function manually setting nr_cells to a lower number.

Best,

Seppe

[SeppeDeWinter]

Hi,

you can use this 6b4bdad function instead. It does not require generating pseudobulks beforehand.

Best,

Seppe

[Umaarasu]

@SeppeDeWinter setting nr_cells= 1 helped resolve the issue.
Thanks!